Tried your tip David on one of my easier scans. Had no idea about this and it seems to work pretty good!
Usually my scans are only one chunk so getting this to work I need to have at least two chunks to be able to get Agisoft to align chunks to begin with, next step would be to merge chunks, correct?
This is what I did, please let me know if there are easier way to do this David:)
Duplicate chunk so I got two chunks
Aling chunks, didnt bother much of the settings just keep them at low pointbased and 1000
Next delete one of the chunks
Do the selection and make sure it's selected when duplicating your chunk again.
Invert the selection on one of the chunks, now you have a exact split when removing respective part.
On one of the chunks I played with grow selection or shrink selection so I got some overlapping just incase when decimating.
Did my decimating and combine chunks with combine model checked.
I also tried and continue splitting and adding more chunks which also worked fine, so you can have different amount of decimation and detail where needed..